SMTL ID : 7ltg.3 (2 other biounits)

STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH APICIDIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: YED.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.188, A:T.191, A:V.194, H2O.1, H2O.5 CA.3: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, F.199, H.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.175, A:D.175, A:D.177, A:H.179, A:S.198

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: L.162, A.187, F.188, T.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.191 Water bridges: A:R.193 PEG.5: 6 residues within 4Å: Chain A: L.165, K.166, Y.167, H.168, Q.169, R.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.169

1 x YED: (3S,6S,9S,15aR)-9-[(2S)-butan-2-yl]-3-(6,6-dihydroxyoctyl)-6-[(1-methoxy-1H-indol-3-yl)methyl]octahydro-2H-pyrido[1,2-a][1,4,7,10]tetraazacyclododecine-1,4,7,10(3H,12H)-tetrone(Non-covalent)

YED.6: 20 residues within 4Å: Chain A: G.28, H.29, P.30, M.31, E.99, D.100, H.141, H.142, G.150, F.151, D.177, H.179, F.206, D.265, R.271, L.272, G.301, G.302, Y.304 Ligands: ZN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.30, A:F.151, A:F.151, A:F.151, A:F.206, A:F.206 Hydrogen bonds: A:D.100, A:D.100, A:D.100, A:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beshore, D.C. et al., Redefining the Histone Deacetylase Inhibitor Pharmacophore: High Potency with No Zinc Cofactor Interaction. Acs Med.Chem.Lett. (2021)

Release Date

2021-05-05

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Histone deacetylase 2

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